# Title     : TODO
# Objective : TODO
# Created by: Administrator
# Created on: 2019/8/12
library(optparse)
library(magrittr)
library(impute)
library(tidyverse)

option_list <- list(
  make_option("--cc", default = "calculate_config.json", type = "character", help = "config file"),
  make_option("--si", default = "1;0", type = "character", help = "step")
)
opt <- parse_args(OptionParser(option_list = option_list))

args <- commandArgs(trailingOnly = F)
scriptPath <- dirname(sub("--file=", "", args[grep("--file", args)]))
source(str_c(scriptPath, "/base.R"))

configJson <- fromJSON(opt$cc)

si <- opt$si %>%
  str_split(";") %>%
  unlist()
step <- si[1] %>%
  as.numeric()

normalMethod  <- configJson$datas$normalMethod[step]
rateStr  <- configJson$datas$area[step]

data <- read_tsv(str_c(step - 1, ".result.txt")) %>%
  rename(Metabolite = 1)

if (normalMethod == "sum") {

  rate <- if (rateStr == "mean") {
    data %>%
      select_at(vars(!starts_with("QC"), -"Metabolite")) %>%
      summarise_all(function(x) {
        sum(x, na.rm = T)
      }) %>%
      mutate(mean = rowMeans(.)) %>%
      .$mean
  }else {
    rateStr %>%
      as.numeric()
  }

  data <- data %>%
    mutate_at(vars(-c("Metabolite")), function(x) {
      sum <- sum(x, na.rm = T)
      x * rate / sum
    })
}else if (normalMethod == "median") {
  data <- data %>%
    mutate_at(vars(-c("Metabolite")), function(x) {
      median <- median(x, na.rm = T)
      x / median
    })
}

outData <- data
outData

write_tsv(outData, str_c(step, ".result.txt"))
write_csv(outData, str_c(step, ".normal.csv"))








